Michelle Coote

Computer Aided Chemical Design

Scripts Downloading Page

last update: 20 Jan 12

All scripts were written by C.Y. Lin, E.I. Izgorodina, D. Brittain, and K. Zhang with additional standard packages from the Comprehensive Perl Archive Network (cpan), except the following subroutines: zmt2xyz, written by J. Labanowski (jkl@ccl.net) in 1997 and makexyz98, written by N. J. R. van Eikema Hommes (hommes@ccc.uni-erlangen.de) in 1997.


Calculate the Solid of Revolution
Please orient your molecule for cone center to (0,0,0), and radical center (0,0,Z) to get the Z axis aligned to the axis of revolution.This program uses Spartan's Van der Waal radii instead of Bondi's standard one. Disc method has been used for numerically summation with an increment of 0.001 Angstrom.
usage: revolution.pl $mol.xyz


Work out the steric parameter of a legend. (includes tolman cone angle)

usage: apex.pl $mol.xyz
Note: Cone center of a legend need to be defined, please read the apex.pl file for more detail. This works for carbon center radical only. For non-carbon center radical, please email for another programs.


Convert basis set from gaussian input into molpro input format

usage: %prog [-b gaussian_basis|-e gaussian_ecp] [-o output_file]


Convert basis set from gaussian output into molpro input format

To use, simply set GFPrint in the gaussian input file, and do g2mbasis.pl $mol.log


This is a easier way to create your conformers!

To use, simply have the bond desired for rotation saved in a file "$mol.bonds"
And given a xyz file that is called "$mol.xyz"
rotbond.pl $mol

If you have a transition structure with elongated bond, you also need to put atom number 1 and 2 that connects the elongated bond, ie
rotbond.pl $mol $tsatom1 $tsatom2

This code can also be used for generating rotational fragments for hindered rotor.

Tunnel Coefficient Spreadsheet

This spreadsheet is a Microsoft Excel file enabling calculation of the tunnel coefficients with the following known variables: forward barrier, reverse barrier, imaginary frequency of the transition state and the temperature for a given reactioin.
M. L. Coote, M. A. Collins and L. Radom, Mol. Phys. 101, 1329-1338 (2003).


T-Chem is the program to calculate thermochemistry data for harmonic oscillator, hindered rotor, and free rotor corrections
C.Y. Lin, E.I. Izgorodina and M.L. Coote. J. Phys. Chem. A. 112, 1956-1964 (2008).


rjsub is used to determine how much time/memory is required to submit a variety of input file on to Raijin. Programs available: Q-Chem, GAMESS, Molpro, ADF, Gaussian


usa is used to submit jobs to Raijin from a local machine. Programs available: Q-Chem, GAMESS, Molpro, ADF, Gaussian Require folder on supercomputer /short/$project/$username/RUN, /short/$project/$username/RETRIEVE and $home/JOB


ComfileCheck is used to check if the geometry in the input file is valid. It return the badness (too many bonds, or bonds is too short) of the geometry.
E. I. Izgorodina , C.Y. Lin, M. L. Coote. Phys. Chem. Chem. Phys. 9, 2507 (2007).


ConfMaker is the fortran program to generate a full conformational space. Need compiler for fortran77.
E. I. Izgorodina , C.Y. Lin, M. L. Coote. Phys. Chem. Chem. Phys. 9, 2507 (2007).


ConfSearch is the ConfSearch program that can be carriered out from a local machine, and copy files back to the local machine when it is done.
E. I. Izgorodina , C.Y. Lin, M. L. Coote. Phys. Chem. Chem. Phys. 9, 2507 (2007).


This can be used in both irc jobs and scan jobs, it returns each of the scan points and the final energy at each point.


this creates Gaussian/Molpro/Q-Chem input files from all sorts of output/input xyz/zmat files.